John Quackenbush

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 28

Top Topics

Restricted Boltzmann Machine

Gene Regulatory

Top Venues

BMC Syst. Biol.

Publications

Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H. Shutta, Kimberly Glass, Dawn L. DeMeo, Camila Miranda Lopes-Ramos, John Quackenbush
BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data. RECOMB (2024)
Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Tina Wipfler, Katherine H. Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth, Helena U. Zacharias, Peter J. Oefner, John Quackenbush, Michael Altenbuchinger
SpaCeNet: Spatial Cellular Networks from Omics Data. RECOMB (2024)
Intekhab Hossain, Jonas Fischer, Rebekka Burkholz, John Quackenbush
Not all tickets are equal and we know it: Guiding pruning with domain-specific knowledge. CoRR (2024)
John Quackenbush
Looking back at the first twenty years of genomics. Quant. Biol. 10 (1) (2022)
Marouen Ben Guebila, Camila M. Lopes-Ramos, Deborah Weighill, Abhijeet Rajendra Sonawane, Rebekka Burkholz, Behrouz Shamsaei, John Platig, Kimberly Glass, Marieke L. Kuijjer, John Quackenbush
GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Res. 50 (D1) (2022)
Alkis Gotovos, Rebekka Burkholz, John Quackenbush, Stefanie Jegelka
Scaling up Continuous-Time Markov Chains Helps Resolve Underspecification. CoRR (2021)
Alkis Gotovos, Rebekka Burkholz, John Quackenbush, Stefanie Jegelka
Scaling up Continuous-Time Markov Chains Helps Resolve Underspecification. NeurIPS (2021)
Rebekka Burkholz, John Quackenbush
Cascade Size Distributions: Why They Matter and How to Compute Them Efficiently. AAAI (2021)
Deborah Weighill, Marouen Ben Guebila, Camila M. Lopes-Ramos, Kimberly Glass, John Quackenbush, John Platig, Rebekka Burkholz
Gene Regulatory Network Inference as Relaxed Graph Matching. AAAI (2021)
Jipeng Qiang, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen
Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer. IEEE Access 8 (2020)
Olga Andreeva, Wei Li, Wei Ding, Marieke L. Kuijjer, John Quackenbush, Ping Chen
Catalysis Clustering with GAN by Incorporating Domain Knowledge. KDD (2020)
Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass
PUMA: PANDA Using MicroRNA Associations. Bioinform. 36 (18) (2020)
Tianyu Kang, Ping Chen, John Quackenbush, Wei Ding
A Novel Deep Learning Model by Stacking Conditional Restricted Boltzmann Machine and Deep Neural Network. KDD (2020)
Lana X. Garmire, Guo-Cheng Yuan, Rong Fan, Gene W. Yeo, John Quackenbush
Session introduction. PSB (2019)
Rebekka Burkholz, John Quackenbush
Cascade Size Distributions and Why They Matter. CoRR (2019)
Sheila M. Gaynor, Ryan Sun, Xihong Lin, John Quackenbush
Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic. Bioinform. 35 (22) (2019)
Tianyu Kang, Kourosh Zarringhalam, Marieke L. Kuijjer, Ping Chen, John Quackenbush, Wei Ding
Clustering on Sparse Data in Non-overlapping Feature Space with Applications to Cancer Subtyping. ICDM (2018)
Daniel Schlauch, Joseph N. Paulson, Albert Young, Kimberly Glass, John Quackenbush
Estimating gene regulatory networks with pandaR. Bioinform. 33 (14) (2017)
Reiko Nishihara, Kimberly Glass, Kosuke Mima, Tsuyoshi Hamada, Jonathan A. Nowak, Zhi Rong Qian, Peter Kraft, Edward L. Giovannucci, Charles S. Fuchs, Andrew T. Chan, John Quackenbush, Shuji Ogino, Jukka-Pekka Onnela
Biomarker correlation network in colorectal carcinoma by tumor anatomic location. BMC Bioinform. 18 (1) (2017)
Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes-Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinform. 18 (1) (2017)
Jipeng Qiang, Wei Ding, John Quackenbush, Ping Chen
Network-based Distance Metric with Application to Discover Disease Subtypes in Cancer. CoRR (2017)
John Platig, Peter J. Castaldi, Dawn L. DeMeo, John Quackenbush
Bipartite Community Structure of eQTLs. PLoS Comput. Biol. 12 (9) (2016)
David G. P. van IJzendoorn, Kimberly Glass, John Quackenbush, Marieke L. Kuijjer
PyPanda: a Python package for gene regulatory network reconstruction. Bioinform. 32 (21) (2016)
Zhaleh Safikhani, Nehme Hachem, Petr Smirnov, Mark Freeman, Anna Goldenberg, Nicolai J. Birkbak, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush, Benjamin Haibe-Kains
. reply. Nat. 540 (7631) (2016)
Solaiappan Manimaran, Heather Selby, Kwame Okrah, Claire Ruberman, Jeffrey T. Leek, John Quackenbush, Benjamin Haibe-Kains, Héctor Corrada Bravo, W. Evan Johnson
BatchQC: interactive software for evaluating sample and batch effects in genomic data. Bioinform. 32 (24) (2016)
Megha Padi, John Quackenbush
Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. BMC Syst. Biol. 9 (2015)
Kimberly Glass, John Quackenbush, Jeremy Kepner
High performance computing of gene regulatory networks using a message-passing model. HPEC (2015)
Kimberly Glass, John Quackenbush, Dimitrios Spentzos, Benjamin Haibe-Kains, Guo-Cheng Yuan
A network model for angiogenesis in ovarian cancer. BMC Bioinform. 16 (2015)
Jen-hwa Chu, Craig P. Hersh, Peter J. Castaldi, Michael H. Cho, Benjamin A. Raby, Nan M. Laird, Russell Bowler, Stephen I. Rennard, Joseph Loscalzo, John Quackenbush, Edwin K. Silverman
Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD. BMC Syst. Biol. 8 (2014)
Kimberly Glass, John Quackenbush, Edwin K. Silverman, Bartolome Celli, Stephen I. Rennard, Guo-Cheng Yuan, Dawn L. DeMeo
Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst. Biol. 8 (2014)
Markus S. Schröder, Daniel Gusenleitner, John Quackenbush, Aedín C. Culhane, Benjamin Haibe-Kains
RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. Bioinform. 29 (5) (2013)
Simon Papillon-Cavanagh, Nicolas De Jay, Nehme Hachem, Catharina Olsen, Gianluca Bontempi, Hugo J. W. L. Aerts, John Quackenbush, Benjamin Haibe-Kains
Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity. J. Am. Medical Informatics Assoc. 20 (4) (2013)
Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai J. Birkbak, Andrew C. Jin, Andrew H. Beck, Hugo J. W. L. Aerts, John Quackenbush
Inconsistency in large pharmacogenomic studies. Nat. 504 (7480) (2013)
Andrew H. Beck, Nicholas W. Knoblauch, Marco M. Hefti, Jennifer Kaplan, Stuart J. Schnitt, Aedín C. Culhane, Markus S. Schröder, Thomas Risch, John Quackenbush, Benjamin Haibe-Kains
Significance Analysis of Prognostic Signatures. PLoS Comput. Biol. 9 (1) (2013)
Aedín C. Culhane, Markus S. Schröder, Razvan Sultana, Shaita C. Picard, Enzo N. Martinelli, Caroline Kelly, Benjamin Haibe-Kains, Misha Kapushesky, Anne-Alyssa St Pierre, William Flahive, Kermshlise C. Picard, Daniel Gusenleitner, Gerald Papenhausen, Niall O'Connor, Mick Correll, John Quackenbush
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res. 40 (Database-Issue) (2012)
Natali Gulbahce, Han Yan, Amélie Dricot, Megha Padi, Danielle Byrdsong, Rachel Franchi, Deok-Sun Lee, Orit Rozenblatt-Rosen, Jessica C. Mar, Michael A. Calderwood, Amy Baldwin, Bo Zhao, Balaji Santhanam, Pascal Braun, Nicolas Simonis, Kyung-Won Huh, Karin Hellner, Miranda Grace, Alyce Chen, Renee Rubio, Jarrod A. Marto, Nicholas A. Christakis, Elliott Kieff, Frederick P. Roth, Jennifer Roecklein-Canfield, James A. DeCaprio, Michael E. Cusick, John Quackenbush, David E. Hill, Karl Münger, Marc Vidal, Albert-László Barabási
Viral Perturbations of Host Networks Reflect Disease Etiology. PLoS Comput. Biol. 8 (6) (2012)
Thomas W. Chittenden, Eleanor Howe, Jennifer M. Taylor, Jessica C. Mar, Martin J. Aryee, Harold Gómez, Razvan Sultana, John C. Braisted, Sarita J. Nair, John Quackenbush, Chris Holmes
nEASE: a method for gene ontology subclassification of high-throughput gene expression data. Bioinform. 28 (5) (2012)
Daniel Gusenleitner, Eleanor Howe, Stefan Bentink, John Quackenbush, Aedín C. Culhane
iBBiG: iterative binary bi-clustering of gene sets. Bioinform. 28 (19) (2012)
Benjamin Haibe-Kains, Catharina Olsen, Amira Djebbari, Gianluca Bontempi, Mick Correll, Christopher Bouton, John Quackenbush
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Res. 40 (Database-Issue) (2012)
Gianluca Bontempi, Benjamin Haibe-Kains, Christine Desmedt, Christos P. Sotiriou, John Quackenbush
Multiple-input multiple-output causal strategies for gene selection. BMC Bioinform. 12 (2011)
Markus S. Schröder, Aedín C. Culhane, John Quackenbush, Benjamin Haibe-Kains
: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinform. 27 (22) (2011)
Fenglong Liu, Joseph White, Corina Antonescu, John Quackenbush
GCOD - GeneChip Oncology Database. BMC Bioinform. 12 (2011)
Eleanor Howe, Raktim Sinha, Daniel Schlauch, John Quackenbush
RNA-Seq analysis in MeV. Bioinform. 27 (22) (2011)
Jarupon Fah Sathirapongsasuti, Hane Lee, Basil A. J. Horst, Georg Brunner, Alistair J. Cochran, Scott Binder, John Quackenbush, Stanley F. Nelson
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinform. 27 (19) (2011)
Jessica C. Mar, Christine A. Wells, John Quackenbush
Defining an informativeness metric for clustering gene expression data. Bioinform. 27 (8) (2011)
Aedín C. Culhane, Thomas Schwarzl, Razvan Sultana, Kermshlise C. Picard, Shaita C. Picard, Tim H. Lu, Katherine R. Franklin, Simon J. French, Gerald Papenhausen, Mick Correll, John Quackenbush
GeneSigDB - a curated database of gene expression signatures. Nucleic Acids Res. 38 (Database-Issue) (2010)
Alex Bateman, John Quackenbush
Editorial. Bioinform. 25 (4) (2009)
Jessica C. Mar, Yasumasa Kimura, Kate Schroder, Katharine M. Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David A. Hume, John Quackenbush
Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinform. 10 (2009)
Martin J. Aryee, José A. Gutiérrez-Pabello, Igor Kramnik, Tapabrata Maiti, John Quackenbush
An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). BMC Bioinform. 10 (2009)
Michael F. Ochs, John Quackenbush, Ramana Davuluri, Habtom W. Ressom
Session Introduction. Pacific Symposium on Biocomputing (2009)
David M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo
Papers on normalization, variable selection, classification or clustering of microarray data. Bioinform. 25 (6) (2009)
Jessica C. Mar, John Quackenbush
Decomposition of Gene Expression State Space Trajectories. PLoS Comput. Biol. 5 (12) (2009)
Amira Djebbari, John Quackenbush
Seeded Bayesian Networks: Constructing genetic networks from microarray data. BMC Syst. Biol. 2 (2008)
Michael F. Ochs, John Quackenbush, Ramana Davuluri
Session Introduction. Pacific Symposium on Biocomputing (2008)
Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, Xiaole Shirley Liu
Microarray blob-defect removal improves array analysis. Bioinform. 23 (8) (2007)
John Quackenbush
Stochasticity and Networks in Genomic Data. BIBE (2007)
Tim F. Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert Jr., Joseph White, Patricia L. Whetzel, Farrell Wymore, Helen E. Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brazma
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinform. 7 (2006)
Agnes P. Chan, Geo Pertea, Foo Cheung, Dan Lee, Li Zheng, Cathy Whitelaw, Ana C. Pontaroli, Phillip SanMiguel, Yinan Yuan, Jeffrey Bennetzen, William Brad Barbazuk, John Quackenbush, Pablo D. Rabinowicz
The TIGR Maize Database. Nucleic Acids Res. 34 (Database-Issue) (2006)
John Quackenbush, Steven Salzberg
It is time to end the patenting of software. Bioinform. 22 (12) (2006)
Yuandan Lee, Jennifer Tsai, S. Sunkara, Svetlana Karamycheva, Geo Pertea, Razvan Sultana, Valentin Antonescu, Agnes P. Chan, Foo Cheung, John Quackenbush
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res. 33 (Database-Issue) (2005)
Adam A. Margolin, Joel Greshock, Tara L. Naylor, Yael Mosse, John M. Maris, Graham Bignell, Alexander I. Saeed, John Quackenbush, Barbara L. Weber
CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinform. 21 (15) (2005)
Amira Djebbari, Svetlana Karamycheva, Eleanor Howe, John Quackenbush
MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. Bioinform. 21 (15) (2005)
Richard Tong, John Quackenbush, Mark Snuffin
Knowledge-Based Access to the Bio-Medical Literature, Ontologically-Grounded Experiments for the TREC 2003 Genomics Track. TREC (2003)
Qiaoping Yuan, Shu Ouyang, Jia Liu, Bernard B. Suh, Foo Cheung, Razvan Sultana, Daniel Lee, John Quackenbush, C. Robin Buell
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res. 31 (1) (2003)
Geo Pertea, Xiaoqiu Huang, Feng Liang, Valentin Antonescu, Razvan Sultana, Svetlana Karamycheva, Yuandan Lee, Joseph White, Foo Cheung, Babak Parvizi, Jennifer Tsai, John Quackenbush
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinform. 19 (5) (2003)
Catherine A. Ball, Gavin Sherlock, Helen E. Parkinson, Philippe Rocca-Serra, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank C. P. Holstege, Martin Ringwald, Paul T. Spellman, Christian J. Stoeckert Jr., Jason E. Stewart, Ronald Taylor, Alvis Brazma, John Quackenbush
An open letter to the scientific journals. Bioinform. 18 (11) (2002)
Alexander Sturn, John Quackenbush, Zlatko Trajanoski
Genesis: cluster analysis of microarray data. Bioinform. 18 (1) (2002)
John Quackenbush, Jennifer Cho, Daniel Lee, Feng Liang, Ingeborg Holt, Svetlana Karamycheva, Babak Parvizi, Geo Pertea, Razvan Sultana, Joseph White
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 29 (1) (2001)
John Quackenbush, Feng Liang, Ingeborg Holt, Geo Pertea, Jonathan Upton
The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res. 28 (1) (2000)